On Wikipedia it says the latest game version is 4.1BB, but on GOG's version in the menu it says 4.0BB, could anyone please explain the difference between these two versions?

They're both unofficial patches and the newer one seems like mostly multiplayer fixes. You can get it here if you'd like: http://www.mediafire.com/?qr5nuq233qxhrtl

From the installer:

"Version 4.1 beta patch includes:

- Sound for host in multiplayer games! (no more excuses if your monarch die while hosting, everyone can host! )
- Option to always allow Monarch Expendable
- Allows 8 Players on direct play launch, such as Gamespy Arcade
- Allows the 5th Race known as Creon on direct play such as, Gamespy Arcade and all the features from the Iron Plague expansion pack (movies can be downloaded apart)
- ironplague.icd no longer used.
- Command line not allowed anymore (3rd party unit makers can instead of using the -disablecavedog... just move the kingdoms.key file out of the kingdoms folder, but remember to put it back to play online)

Version 4.0 patch includes:

- 500 units limit
- More than 500 maps bug fix
- Allows more than one AI per person in mutliplayer games
- Direct Play launch on ironplague.icd allows the Creon race on multiplayer games"

Weirdly enough GOG only added 4.0...

Ehm... but then what is THAT?

http://www.moddb.com/games/total-annihilation-kingdoms/downloads/ta-kingdoms-v30-patch-darien-crusades

As far as I know, 3.0 is the last official patch, and the Darien Crusades are some additional maps that Cavedog made. It used to be on the official website: https://web.archive.org/web/20000302145005/http://www.cavedog.com/ta-kingdoms/patch.html

Ah, I see, 3.0 is the latest official patch for vanilla TAK game, without Iron Plague add-on.

Probably. Some YouTube videos show Iron Plague at 3.0, and considering it already included some units for non-Creon factions that were downloadable from Cavedog's website, it's possible patch 3.0 was basically a compatibility patch for vanilla Kingdoms so it can connect to non-Creon matches in Iron Plague.

So does GOG version - 4.0, 4.1 or whatever it is - contain all the stuff one could need to enjoy TAK?

GOG has 4.0, made by AxlRose (Sage's brother).
They are patches, not mods! by the way.

Read the second post in this thread to know what each does.